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2.
Cancers (Basel) ; 13(5)2021 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-33806447

RESUMO

Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit amplifying-like, and differentiated CRC cells resemble differentiation states of normal intestinal epithelial cells. Strikingly, identified subpopulations differ in proliferative activity and metabolic state. In summary, we here show at single-cell resolution that transcriptional heterogeneity identifies functional states during TIC differentiation. Furthermore, identified expression signatures are linked to patient prognosis. Targeting transcriptional states associated to cancer cell differentiation might unravel novel vulnerabilities in human CRC.

3.
Epigenetics ; : 1-16, 2021 Feb 17.
Artigo em Inglês | MEDLINE | ID: mdl-33595421

RESUMO

Genome-wide association studies (GWAS) have identified SNPs linked with lung cancer risk. Our aim was to discover the genes, non-coding RNAs, and regulatory elements within GWAS-identified risk regions that are deregulated in non-small cell lung carcinoma (NSCLC) to identify novel, clinically targetable genes and mechanisms in carcinogenesis. A targeted bisulphite-sequencing approach was used to comprehensively investigate DNA methylation changes occurring within lung cancer risk regions in 17 NSCLC and adjacent normal tissue pairs. We report differences in differentially methylated regions between adenocarcinoma and squamous cell carcinoma. Among the minimal regions found to be differentially methylated in at least 50% of the patients, 7 candidates were replicated in 2 independent cohorts (n = 27 and n = 87) and the potential of 6 as methylation-dependent regulatory elements was confirmed by functional assays. This study contributes to understanding the pathways implicated in lung cancer initiation and progression, and provides new potential targets for cancer treatment.

4.
Brief Bioinform ; 2021 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-33589928

RESUMO

This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

6.
Am J Pathol ; 191(4): 602-617, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33497701

RESUMO

Solitary fibrous tumors (SFTs) harbor recurrent NAB2-STAT6 gene fusions, promoting constitutional up-regulation of oncogenic early growth response 1 (EGR1)-dependent gene expression. SFTs with the most common canonical NAB2 exon 4-STAT6 exon 2 fusion variant are often located in the thorax (pleuropulmonary) and are less cellular with abundant collagen. In contrast, SFTs with NAB2 exon 6-STAT6 exon 16/17 fusion variants typically display a cellular round to ovoid cell morphology and are often located in the deep soft tissue of the retroperitoneum and intra-abdominal pelvic region or in the meninges. Here, we employed next-generation sequencing-based gene expression profiling to identify significant differences in gene expression associated with anatomic localization and NAB2-STAT6 gene fusion variants. SFTs with the NAB2 exon 4-STAT6 exon 2 fusion variant showed a transcriptional signature enriched for genes involved in DNA binding, gene transcription, and nuclear localization, whereas SFTs with the NAB2 exon 6-STAT6 exon 16/17 fusion variants were enriched for genes involved in tyrosine kinase signaling, cell proliferation, and cytoplasmic localization. Specific transcription factor binding motifs were enriched among differentially expressed genes in SFTs with different fusion variants, implicating co-transcription factors in the modification of chimeric NGFI-A binding protein 2 (NAB2)-STAT6-dependent deregulation of EGR1-dependent gene expression. In summary, this study establishes a potential molecular biologic basis for clinicopathologic differences in SFTs with distinct NAB2-STAT6 gene fusion variants.

7.
Nat Immunol ; 22(2): 229-239, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33398179

RESUMO

In chronic hepatitis C virus (HCV) infection, exhausted HCV-specific CD8+ T cells comprise memory-like and terminally exhausted subsets. However, little is known about the molecular profile and fate of these two subsets after the elimination of chronic antigen stimulation by direct-acting antiviral (DAA) therapy. Here, we report a progenitor-progeny relationship between memory-like and terminally exhausted HCV-specific CD8+ T cells via an intermediate subset. Single-cell transcriptomics implicated that memory-like cells are maintained and terminally exhausted cells are lost after DAA-mediated cure, resulting in a memory polarization of the overall HCV-specific CD8+ T cell response. However, an exhausted core signature of memory-like CD8+ T cells was still detectable, including, to a smaller extent, in HCV-specific CD8+ T cells targeting variant epitopes. These results identify a molecular signature of T cell exhaustion that is maintained as a chronic scar in HCV-specific CD8+ T cells even after the cessation of chronic antigen stimulation.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Hepacivirus/imunologia , Hepatite C Crônica/imunologia , Memória Imunológica/genética , Transcriptoma , Antígenos Virais/imunologia , Antivirais/uso terapêutico , Linfócitos T CD8-Positivos/metabolismo , Linfócitos T CD8-Positivos/virologia , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Hepacivirus/efeitos dos fármacos , Hepatite C Crônica/tratamento farmacológico , Hepatite C Crônica/genética , Hepatite C Crônica/virologia , Interações Hospedeiro-Patógeno , Humanos , Fenótipo , Indução de Remissão , Análise de Célula Única , Resultado do Tratamento
8.
Nucleic Acids Res ; 49(5): e29, 2021 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-33330940

RESUMO

Optogenetic control of CRISPR-Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and engineered, the need for straightforward strategies to control their activity via exogenous stimuli persists. The Cas9 from Neisseria meningitidis (Nme) is a particularly small and target-specific Cas9 orthologue, and thus of high interest for in vivo genome editing applications. Here, we report the first optogenetic tool to control NmeCas9 activity in mammalian cells via an engineered, light-dependent anti-CRISPR (Acr) protein. Building on our previous Acr engineering work, we created hybrids between the NmeCas9 inhibitor AcrIIC3 and the LOV2 blue light sensory domain from Avena sativa. Two AcrIIC3-LOV2 hybrids from our collection potently blocked NmeCas9 activity in the dark, while permitting robust genome editing at various endogenous loci upon blue light irradiation. Structural analysis revealed that, within these hybrids, the LOV2 domain is located in striking proximity to the Cas9 binding surface. Together, our work demonstrates optogenetic regulation of a type II-C CRISPR effector and might suggest a new route for the design of optogenetic Acrs.


Assuntos
Proteína 9 Associada à CRISPR/antagonistas & inibidores , Proteína 9 Associada à CRISPR/química , Sistemas CRISPR-Cas , Edição de Genes/métodos , Neisseria meningitidis/enzimologia , Optogenética/métodos , Linhagem Celular , Células HEK293 , Humanos , Luz , Modelos Moleculares , Engenharia de Proteínas , Proteínas/química , Proteínas/efeitos da radiação
9.
Nat Neurosci ; 2020 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-33257876

RESUMO

The newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic respiratory disease. Moreover, thromboembolic events throughout the body, including in the CNS, have been described. Given the neurological symptoms observed in a large majority of individuals with COVID-19, SARS-CoV-2 penetrance of the CNS is likely. By various means, we demonstrate the presence of SARS-CoV-2 RNA and protein in anatomically distinct regions of the nasopharynx and brain. Furthermore, we describe the morphological changes associated with infection such as thromboembolic ischemic infarction of the CNS and present evidence of SARS-CoV-2 neurotropism. SARS-CoV-2 can enter the nervous system by crossing the neural-mucosal interface in olfactory mucosa, exploiting the close vicinity of olfactory mucosal, endothelial and nervous tissue, including delicate olfactory and sensory nerve endings. Subsequently, SARS-CoV-2 appears to follow neuroanatomical structures, penetrating defined neuroanatomical areas including the primary respiratory and cardiovascular control center in the medulla oblongata.

10.
Nat Biotechnol ; 2020 Dec 24.
Artigo em Inglês | MEDLINE | ID: mdl-33361824

RESUMO

In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.

11.
Nat Commun ; 11(1): 6434, 2020 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-33339831

RESUMO

Glioblastoma frequently exhibits therapy-associated subtype transitions to mesenchymal phenotypes with adverse prognosis. Here, we perform multi-omic profiling of 60 glioblastoma primary tumours and use orthogonal analysis of chromatin and RNA-derived gene regulatory networks to identify 38 subtype master regulators, whose cell population-specific activities we further map in published single-cell RNA sequencing data. These analyses identify the oligodendrocyte precursor marker and chromatin modifier SOX10 as a master regulator in RTK I-subtype tumours. In vitro functional studies demonstrate that SOX10 loss causes a subtype switch analogous to the proneural-mesenchymal transition observed in patients at the transcriptomic, epigenetic and phenotypic levels. SOX10 repression in an in vivo syngeneic graft glioblastoma mouse model results in increased tumour invasion, immune cell infiltration and significantly reduced survival, reminiscent of progressive human glioblastoma. These results identify SOX10 as a bona fide master regulator of the RTK I subtype, with both tumour cell-intrinsic and microenvironmental effects.


Assuntos
Neoplasias Encefálicas/classificação , Neoplasias Encefálicas/genética , Epigenoma , Glioblastoma/classificação , Glioblastoma/genética , Fatores de Transcrição SOXE/metabolismo , Linhagem Celular Tumoral , Metilação de DNA/genética , Elementos Facilitadores Genéticos/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Mesoderma/patologia , Pessoa de Meia-Idade , Fenótipo , Reprodutibilidade dos Testes , Fatores de Transcrição SOXE/genética
12.
Artigo em Inglês | MEDLINE | ID: mdl-33222322

RESUMO

Different mutational processes leave characteristic patterns of somatic mutations in the genome that can be identified as mutational signatures. Determining the contributions of mutational signatures to cancer genomes allows not only to reconstruct the etiology of somatic mutations, but can also be used for improved tumor classification and support therapeutic decisions. We here present the R package YAPSA (Yet Another Package for Signature Analysis) to deconvolute the contributions of mutational signatures to tumor genomes. YAPSA provides in-built collections from the COSMIC and PCAWG SNV signature sets as well as the PCAWG Indel signatures and employs signature-specific cutoffs to increase sensitivity and specificity. Furthermore, YAPSA allows to determine 95% confidence intervals for signature exposures, to perform constrained stratified signature analyses to obtain enrichment and depletion patterns of the identified signatures and, when applied to whole exome sequencing data, to correct for the triplet content of individual target capture kits. With this functionality, YAPSA has proved to be a valuable tool for analysis of mutational signatures in molecular tumor boards in a precision oncology context. YAPSA is available at R/Bioconductor (http://bioconductor.org/packages/3.12/bioc/html/YAPSA.html). This article is protected by copyright. All rights reserved.

13.
Clin Res Cardiol ; 2020 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-33211156

RESUMO

BACKGROUND: The early recognition of paroxysmal atrial fibrillation (pAF) is a major clinical challenge for preventing thromboembolic events. In this prospective and multicentric study we evaluated prediction scores for the presence of pAF, calculated from non-invasive medical history and echocardiographic parameters, in patients with unknown AF status. METHODS: The 12-parameter score with parameters age, LA diameter, aortic root diameter, LV,ESD, TDI A', heart frequency, sleep apnea, hyperlipidemia, type II diabetes, smoker, ß-blocker, catheter ablation, and the 4-parameter score with parameters age, LA diameter, aortic root diameter and TDI A' were tested. Presence of pAF was verified by continuous electrocardiogram (ECG) monitoring for up to 21 days in 305 patients. RESULTS: The 12-parameter score correctly predicted pAF in all 34 patients, in which pAF was newly detected by ECG monitoring. The 12- and 4-parameter scores showed sensitivities of 100% and 82% (95%-CI 65%, 93%), specificities of 75% (95%-CI 70%, 80%) and 67% (95%-CI 61%, 73%), and areas under the receiver operating characteristic (ROC) curves of 0.84 (95%-CI 0.80, 0.88) and 0.81 (95%-CI 0.74, 0.87). Furthermore, properties of AF episodes and durations of ECG monitoring necessary to detect pAF were analysed. CONCLUSIONS: The prediction scores adequately detected pAF using variables readily available during routine cardiac assessment and echocardiography. The model scores, denoted as ECHO-AF scores, represent simple, highly sensitive and non-invasive tools for detecting pAF that can be easily implemented in the clinical practice and might serve as screening test to initiate further diagnostic investigations for validating the presence of pAF. Prospective validation of a novel prediction model for paroxysmal atrial fibrillation based on echocardiography and medical history parameters by long-term Holter ECG.

14.
Gastroenterology ; 2020 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-33212097

RESUMO

BACKGROUND AND AIMS: Molecular evidence of cellular heterogeneity in the human exocrine pancreas has not been yet established, due to the local concentration and cascade of hydrolytic enzymes that can rapidly degrade cells and RNA upon pancreatic resection. We sought to better understand the heterogeneity and cellular composition of the pancreas in neonates and adults in healthy and diseased conditions using single cell sequencing approaches. METHODS: We innovated single-nucleus RNA sequencing protocols and profiled more than 120,000 cells from pancreata of adult and neonatal human donors. We validated the single nucleus findings using RNA-FISH, in situ sequencing and computational approaches. RESULTS: We created the first comprehensive atlas of human pancreas cells, including epithelial and non-epithelial constituents and uncovered three distinct acinar cell types, with possible implications for homeostatic and inflammatory processes of the pancreas. The comparison with neonatal sNuc-seq data revealed a different cellular composition of the endocrine tissue, highlighting tissue dynamics occurring during development. By applying spatial cartography, involving cell proximity mapping through in situ sequencing, we found evidence of specific cell type neighborhoods, dynamic topographies in the endocrine and exocrine pancreas, and principles of morphological organization of the organ. Furthermore, similar analyses in chronic pancreatitis biopsies revealed the presence of acinar-REG+ cells, a reciprocal association between macrophages and activated stellate cells, and a new potential role of Tuft cells in this disease. CONCLUSIONS: Our human pancreas cell atlas can be interrogated to understand pancreatic cell biology and provides a crucial reference set for comparisons with diseased tissue samples to map the cellular foundations of pancreatic diseases.Interactive exploration tool and data download: http://singlecell.charite.de/pancreas. Raw sequencing access-protected data on European Genome-phenome Archive (https://www.ebi.ac.uk/ega/home): EGAS00001004653. In Situ Sequencing raw data: 10.6084/m9.figshare.12173232.

15.
Cancer Discov ; 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33060108

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. Methylationlow tumors are characterized by higher expression of endogenous retroviral (ERV) transcripts and dsRNA sensors which leads to a cell intrinsic activation of an interferon signature (IFNsign). This results in a pro-tumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells preserve lineage traits, respective of normal ductal or acinar pancreatic cells. Moreover, ductal-derived KrasG12D/Trp53-/- mouse PDACs show higher expression of IFNsign compared to acinar-derived counterparts. Collectively, our data point to two different origins and etiologies of human PDACs, with the aggressive Methylationlow/IFNsignhigh subtype potentially targetable by agents blocking intrinsic IFN-signaling.

17.
Nat Commun ; 11(1): 5040, 2020 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-33028839

RESUMO

Bringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole genomes sequenced over several years in different sequencing centres requires a framework to compare the quality of these sequences. We used the Pan-Cancer Analysis of Whole Genomes cohort as a test case to construct such a framework. This cohort contains whole cancer genomes of 2832 donors from 18 sequencing centres. We developed a non-redundant set of five quality control (QC) measurements to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses and allow for exclusion of samples of poor quality. We have found that this is an effective framework of quality measures. The implementation of the framework is available at: https://dockstore.org/containers/quay.io/jwerner_dkfz/pancanqc:1.2.2 .


Assuntos
Genoma Humano/genética , Genômica/normas , Neoplasias/genética , Controle de Qualidade , Mapeamento Cromossômico/normas , Cromossomos Humanos/genética , Análise Mutacional de DNA/normas , Feminino , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Masculino , Mutação , Software , Sequenciamento Completo do Genoma/normas
18.
Stud Health Technol Inform ; 270: 443-447, 2020 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-32570423

RESUMO

Current high-throughput sequencing technologies allow us to acquire entire genomes in a very short time and at a relatively sustainable cost, thus resulting in an increasing diffusion of genetic test capabilities, in specialized clinical laboratories and research centers. In contrast, it is still limited the impact of genomic information on clinical decisions, as an effective interpretation is a challenging task. From the technological point of view, genomic data are big in size, have a complex granular nature and strongly depend on the computational steps of the generation and processing workflows. This article introduces our work to create the openEHR Genomic Project and the set of genomic information models we developed to catch such complex structure and to preserve data provenance efficiently in a machine-readable format. The models support clinical actionability of data, by improving their quality, fostering interoperability and laying the basis for re-usability.


Assuntos
Registros Eletrônicos de Saúde , Genômica , Testes Genéticos , Fluxo de Trabalho
19.
Nat Biotechnol ; 38(8): 970-979, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32591762

RESUMO

To investigate the immune response and mechanisms associated with severe coronavirus disease 2019 (COVID-19), we performed single-cell RNA sequencing on nasopharyngeal and bronchial samples from 19 clinically well-characterized patients with moderate or critical disease and from five healthy controls. We identified airway epithelial cell types and states vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In patients with COVID-19, epithelial cells showed an average three-fold increase in expression of the SARS-CoV-2 entry receptor ACE2, which correlated with interferon signals by immune cells. Compared to moderate cases, critical cases exhibited stronger interactions between epithelial and immune cells, as indicated by ligand-receptor expression profiles, and activated immune cells, including inflammatory macrophages expressing CCL2, CCL3, CCL20, CXCL1, CXCL3, CXCL10, IL8, IL1B and TNF. The transcriptional differences in critical cases compared to moderate cases likely contribute to clinical observations of heightened inflammatory tissue damage, lung injury and respiratory failure. Our data suggest that pharmacologic inhibition of the CCR1 and/or CCR5 pathways might suppress immune hyperactivation in critical COVID-19.


Assuntos
Infecções por Coronavirus/patologia , Infecções por Coronavirus/fisiopatologia , Pneumonia Viral/patologia , Pneumonia Viral/fisiopatologia , Sistema Respiratório/patologia , Análise de Célula Única , Transcriptoma , Adulto , Idoso , Líquido da Lavagem Broncoalveolar/virologia , Comunicação Celular , Diferenciação Celular , Infecções por Coronavirus/virologia , Células Epiteliais/patologia , Células Epiteliais/virologia , Feminino , Humanos , Sistema Imunitário/patologia , Inflamação/imunologia , Inflamação/patologia , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Pandemias , Peptidil Dipeptidase A/genética , Pneumonia Viral/virologia , Sistema Respiratório/imunologia , Sistema Respiratório/virologia , Índice de Gravidade de Doença
20.
Nat Chem Biol ; 16(7): 725-730, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32284602

RESUMO

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, to improve its efficacy on different targets. We first show that inserting exogenous protein domains into a selected AcrIIC1 surface site dramatically enhances inhibition of Neisseria meningitidis (Nme)Cas9. Then, applying structure-guided design to the Cas9-binding surface, we converted AcrIIC1 into AcrIIC1X, a potent inhibitor of the Staphylococcus aureus (Sau)Cas9, an orthologue widely applied for in vivo genome editing. Finally, to demonstrate the utility of AcrIIC1X for genome engineering applications, we implemented a hepatocyte-specific SauCas9 ON-switch by placing AcrIIC1X expression under regulation of microRNA-122. Our work introduces designer Acrs as important biotechnological tools and provides an innovative strategy to safeguard CRISPR technologies.


Assuntos
Proteína 9 Associada à CRISPR/genética , Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Edição de Genes/métodos , MicroRNAs/genética , Engenharia de Proteínas/métodos , Sequência de Aminoácidos , Proteína 9 Associada à CRISPR/metabolismo , Linhagem Celular Tumoral , Genoma Humano , Células HEK293 , Hepatócitos/citologia , Hepatócitos/metabolismo , Humanos , MicroRNAs/metabolismo , Modelos Moleculares , Mutagênese Insercional , Neisseria meningitidis/enzimologia , Neisseria meningitidis/genética , Plasmídeos/química , Plasmídeos/metabolismo , Domínios Proteicos , Estrutura Secundária de Proteína , RNA Guia/genética , RNA Guia/metabolismo , Staphylococcus aureus/enzimologia , Staphylococcus aureus/genética
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